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- PDB-3exr: Crystal structure of KGPDC from Streptococcus mutans -

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Basic information

Entry
Database: PDB / ID: 3exr
TitleCrystal structure of KGPDC from Streptococcus mutans
ComponentsRmpD (Hexulose-6-phosphate synthase)
KeywordsLYASE / beta barrel
Function / homology
Function and homology information


3-dehydro-L-gulonate-6-phosphate decarboxylase activity / L-ascorbic acid catabolic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' pyrimidine nucleobase biosynthetic process / one-carbon metabolic process / metal ion binding
Similarity search - Function
HPS/KGPDC domain / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLi, G.L. / Liu, X. / Li, L.F. / Su, X.D.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Open-closed conformational change revealed by the crystal structures of 3-keto-L-gulonate 6-phosphate decarboxylase from Streptococcus mutans
Authors: Li, G.L. / Liu, X. / Nan, J. / Brostromer, E. / Li, L.F. / Su, X.D.
History
DepositionOct 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2018Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.version
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RmpD (Hexulose-6-phosphate synthase)
B: RmpD (Hexulose-6-phosphate synthase)
C: RmpD (Hexulose-6-phosphate synthase)
D: RmpD (Hexulose-6-phosphate synthase)


Theoretical massNumber of molelcules
Total (without water)95,4014
Polymers95,4014
Non-polymers00
Water14,808822
1
A: RmpD (Hexulose-6-phosphate synthase)
C: RmpD (Hexulose-6-phosphate synthase)


Theoretical massNumber of molelcules
Total (without water)47,7002
Polymers47,7002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-8.3 kcal/mol
Surface area17690 Å2
MethodPISA
2
B: RmpD (Hexulose-6-phosphate synthase)
D: RmpD (Hexulose-6-phosphate synthase)


Theoretical massNumber of molelcules
Total (without water)47,7002
Polymers47,7002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-7.8 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.830, 127.230, 130.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
RmpD (Hexulose-6-phosphate synthase) / 3-keto-L-gulonate 6-phosphate decarboxylase


Mass: 23850.229 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: ulaD / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q93DA8, 3-dehydro-L-gulonate-6-phosphate decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M KCl, 0.05M HEPES, pH7.5, 35%(v/v) pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9798 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 158531 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.605 Å2 / Rmerge(I) obs: 0.083
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.5-1.590.5492.81317462461396.4
1.59-1.70.4264.416701724087100
1.7-1.840.2966.616012622436100
1.84-2.010.29.914793020704100
2.01-2.250.12117.21364551873099.8
2.25-2.60.08424.51214191661799.8
2.6-3.180.05434.110197214124100
3.18-4.480.04338.1800941107299.9
4.480.03344.341564614896.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EXT

3ext


Resolution: 1.7→45.64 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.196 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.815 / SU B: 6.388 / SU ML: 0.093 / SU R Cruickshank DPI: 0.154 / SU Rfree: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 5473 5 %RANDOM
Rwork0.206 ---
obs0.208 110108 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 45.86 Å2 / Biso mean: 17.915 Å2 / Biso min: 6.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6448 0 0 822 7270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226547
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.9488879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.435854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31525.277271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61151102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7821532
X-RAY DIFFRACTIONr_chiral_restr0.0890.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024872
X-RAY DIFFRACTIONr_nbd_refined0.2020.23066
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24560
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2580
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.236
X-RAY DIFFRACTIONr_mcbond_it1.1981.54344
X-RAY DIFFRACTIONr_mcangle_it1.52526756
X-RAY DIFFRACTIONr_scbond_it2.30532482
X-RAY DIFFRACTIONr_scangle_it3.324.52123
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 398 -
Rwork0.228 7697 -
all-8095 -
obs--100 %

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